There are two main types of heat pipes used in popular aftermarket coolers, they are groove and powder. Groove heat pipes are very susceptible to gravity while powder heat pipes are less so. To achieve best performance in either heat pipe technology, they need to be placed horizontally or have the heat source side located below the other end of the heat pipe. We recommend choosing and installing components with heat pipes carefully by taking into consideration of the following examples:
Motherboard:

The orientation of an enthusiast motherboard in a normal ATX case

The orientation of an enthusiast motherboard in the ##
As the illustrations above show, most enthusiast motherboards with heat pipes will work fine in the ##, the heat source is located below other parts of the heat pipe.
CPU cooler:
Horizontal style cooler



Good orientation
Good orientation
Bad orientation
Many CPU coolers can be rotated when installing on motherboards, the illustration here shows a SilverStone NT06-E
VGA cooler
The illustration here shows a VGA cooler that will not work well in the ## because the heat source side (touching the GPU) ends up being located higher than the other end.